Variant report

Variant	rs17051280
Chromosome Location	chr4:121839142-121839143
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:121832110..121834901-chr4:121836477..121839157,3	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10034779	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11931234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11935242	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11939905	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11942376	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11942389	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1450476	0.85[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs1450478	1.00[CHB][hapmap]
rs17051268	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs17051269	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs17051270	0.85[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs17051274	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2278811	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2667188	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2667195	0.92[CHD][hapmap]
rs3115311	0.92[CHD][hapmap]
rs343167	0.92[CHD][hapmap]
rs343168	0.92[CHD][hapmap]
rs343170	0.92[CHD][hapmap]
rs3761726	0.91[ASN][1000 genomes]
rs4833688	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs55930284	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55962052	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56004809	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56270962	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56339840	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60983006	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73843656	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73843658	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73843660	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs885460	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998094	chr4:121504565-122374203	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17051280	NDST3	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:121798200-121842400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:121812000-121839400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr4:121812800-121839800	Weak transcription	Psoas Muscle	Psoas
4	chr4:121813400-121839400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:121813400-121841600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr4:121813600-121839800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr4:121813800-121842400	Weak transcription	NHEK	skin
8	chr4:121814200-121839800	Weak transcription	Pancreas	Pancrea
9	chr4:121814600-121840000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:121814600-121842600	Weak transcription	Right Ventricle	heart
11	chr4:121815200-121839800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:121818000-121842400	Weak transcription	NH-A	brain
13	chr4:121821000-121839800	Weak transcription	Fetal Muscle Leg	muscle
14	chr4:121821200-121840000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr4:121821400-121839800	Weak transcription	Fetal Stomach	stomach
16	chr4:121823800-121842400	Weak transcription	HSMM	muscle
17	chr4:121824800-121840400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr4:121825000-121839800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:121825000-121839800	Weak transcription	Osteobl	bone
20	chr4:121825000-121842600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr4:121825200-121839200	Weak transcription	Fetal Intestine Small	intestine
22	chr4:121825200-121839800	Weak transcription	Aorta	Aorta
23	chr4:121825600-121842400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr4:121827600-121842400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:121828000-121839800	Weak transcription	NHDF-Ad	bronchial
26	chr4:121829600-121839400	Weak transcription	Fetal Intestine Large	intestine
27	chr4:121830600-121839400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr4:121833600-121839800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr4:121836800-121840000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr4:121837000-121842800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr4:121837200-121839800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr4:121837200-121839800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr4:121837400-121842600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr4:121838200-121839800	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr4:121838400-121839200	Weak transcription	Fetal Lung	lung
36	chr4:121838400-121839400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr4:121838400-121839400	Weak transcription	Fetal Kidney	kidney
38	chr4:121838400-121839800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr4:121838400-121839800	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr4:121838400-121839800	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr4:121838400-121839800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr4:121838400-121839800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr4:121838400-121839800	Weak transcription	Left Ventricle	heart
44	chr4:121838400-121839800	Weak transcription	Ovary	ovary
45	chr4:121838400-121840000	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr4:121838400-121840200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr4:121838400-121840800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr4:121838400-121841200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr4:121838400-121841200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr4:121838400-121841200	Weak transcription	NHLF	lung

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